GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocD in Desulfovibrio vulgaris Hildenborough

Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate 208688 DVU3168 glutamate-1-semialdehyde-2,1-aminomutase

Query= BRENDA::P04182
         (439 letters)



>lcl|MicrobesOnline__882:208688 DVU3168
           glutamate-1-semialdehyde-2,1-aminomutase
          Length = 423

 Score =  125 bits (313), Expect = 3e-33
 Identities = 109/342 (31%), Positives = 161/342 (47%), Gaps = 26/342 (7%)

Query: 59  PVALERGKGIYMWDVEGRQYFDFLSAYGAVSQGHCHPKIIEAMKSQVDKLTLTSRAFYNN 118
           P+ + R  G  +  V+G  + DF+ ++G +  GH HP++  A+ + VD+ T       + 
Sbjct: 34  PLFIARAAGSRLHTVDGETFIDFVESWGPMLLGHTHPEVTAAVHAAVDRGTSYGAPCEDE 93

Query: 119 VLGEYEEYITKLFNYNKVLPMNTGVEAGETACKLARRWGYTVKGIQKYKAKIVFAVGNFW 178
           V+    + +  L   + V  +N+G EA  +A +LAR  GYT +       K+V  VG + 
Sbjct: 94  VVLA-AKVVDALPGVDMVRMVNSGTEATMSALRLAR--GYTGR------TKLVKFVGCYH 144

Query: 179 GRT---LSAVSSSTDPTSYDGFGPFMPGFET-----IPYNDLPALER--ALQDPNVAAFM 228
           G     L++  S     S  G  P +P          PYNDL A++   AL   ++AA +
Sbjct: 145 GHADPFLASAGSGVATLSIPGT-PGVPESTVRDTLLAPYNDLAAVKDLFALHGKDIAAII 203

Query: 229 VEPIQGEAGVIVPDPGYLTGVRELCTRHQVLFIADEIQTGLARTGRWLAVDHENVRPDIV 288
           VE + G  G++ P  G+L G+RELC +H  L I DE+ TG  R     A     + PD+ 
Sbjct: 204 VEAVAGNMGLVPPKAGFLEGLRELCDQHGALLIFDEVITGF-RVSFGGAQQRFGITPDLT 262

Query: 289 LLGKALSGGLYPVSAVLCDDDIMLTIKP-GE--HGSTYGGNPLGCRIAIAALEVLEEEHL 345
            LGK + GGL PV A     +IM  I P GE     T  GNPL     IA L+VL     
Sbjct: 263 TLGKIIGGGL-PVGAYGGKREIMQRIAPCGEVYQAGTLSGNPLAMAAGIATLDVLSRSDY 321

Query: 346 AENADKMGAILRKELMKLPSDVVTAVRGKGLLNAIVIRETKD 387
           A    ++ A + KEL  +       VR   L +   +  T D
Sbjct: 322 AGLEARVAAFV-KELEAILKGKGVPVRINTLASMFTVFFTND 362


Lambda     K      H
   0.319    0.137    0.406 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 409
Number of extensions: 24
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 439
Length of database: 423
Length adjustment: 32
Effective length of query: 407
Effective length of database: 391
Effective search space:   159137
Effective search space used:   159137
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory